I wrote a forum entry here (https://www.rosettacommons.org/node/10258) asking about details on RosettaDesign, and I am continuing the conversation here since I ran my script on several structures and got different results and I want a better understanding.
Please find attached a summery of the results. If you look closely you can see the green relaxed structure on the bottom left (sorry if it is not clear).
It seems that the Abinitio folding is dependent on the backbone more than the sequence? correct/wrong?
I have analysed the 3mer and 9mer fragments for each structure and they all give a final average RMSD of 1-3.
My questions are:
- How can I improve my RosettaDesign protocol to take a protein’s structure and design it to give me a funnel shaped Abinitio plot result? What am I doing wrong? What can I improve?
- Are there protein structures than cannot be folded by Abinitio? Even if they are between 80-150AA, compact, and full of secondary structures? which means Abinitio will not get a funnel no matter how good I RosettaDesign it?